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Organizing My Research Life [Updated]

[The following is an updated version of this blog post. Since that one gets a couple hundred hits a month, I figure someone somewhere must find it useful, and since I’ve changed a few things within the last year–especially by using a nifty new syncing feature in Zotero–I thought I’d update.]

This is the latest configuration in my quest to find, store, organize, and access scholarly information in the safest and most efficient way possible. I’ll focus on four productivity tools: the LibX toolbar, Dropbox, Calibre, and Zotero (the reason for this order will be more obvious below). Plus there’s an addendum on Evernote and Evernote Clearly.

LibX allows libraries to build a customized library application that runs as an extension in Google Chrome or an add-on in Mozilla Firefox. It allows users to do various searches directly from the application. Some of the obvious searches are for a library catalog, WorldCat, Web of Science, or large aggregator databases, but other searches can be set up. For example, as you can see in the image below of the Princeton University Library version, users can search for databases by title or search for ejournals by title. The links can be to whatever you want, and our version has links to the library home page, ILL, reserves, and our reference chat service among other things.

Once I started using this, I have almost no need to ever go to the library website anymore. (Which is a pity, because we’re releasing a new website this summer. I was on the redesign committee, and we stole every good idea any library had and put them together pretty smoothly as far as I’m concerned.)

Once you find stuff, you have to store it somewhere, and after experimenting with multiple syncing applications I’ve finally settled on Dropbox exclusively. The free storage is 2GB (although with accepted referrals you can get that up to 18GB). I went with the Pro option of 100GB option for $99/year. Right now I use about 30GB on average, but the Pro option allows uploading of unlimited file sizes, so I can transfer video files or large numbers of music files among computers easily. For impecunious grad students (or even impecunious librarians), I might suggest a cheaper option, but it’s worth the $99/year for my peace of mind. Also, I’ve used Dropbox on multiple devices and operating systems and it’s never failed me. Now everything I have is backed up in the cloud and on every computer that I use, so there’s little chance of losing anything. [For cheaper options, Google Drive offers 25GB for $30/year and SugarSync offers 60GB for $75/year. Or you could set up 32 separate email accounts and send yourself Dropbox referrals to get the 18GB. I realize Google Drive offers 100GB for only $60/year, but I’m doing my best to spread my electronic eggs into as many baskets as possible rather than rely on Google for everything.]

Once you have Dropbox or some other syncing application set up, it’s time to think about managing edocuments. I use Calibre Ebook Management. I call it an edocument manager because it allows you to import ebub, mobi, PDF, Doc, DocX, Txt, and just about any other text based document. Once documents are imported, you can edit the metadata, tag them by subject, add notes, and even convert them among formats.( Got an epub you want to read on a Kindle? This is the program for you.) Calibre makes it very easy to organize and find documents.

The other nice thing is the way it imports them. Instead of just importing the metadata while still pointing to the original folder where you had the file, Calibre imports the entire file into a folder called by default “Calibre Library.” By going to the Preferences and choosing “Run Welcome Wizard,” you can specify where the folder should be. Here’s what it looks like for me:

Notice that I keep my Calibre Library in Dropbox. What that means is that every document I import to Calibre is now synced in the cloud and on every other computer I have Dropbox on. If I’m at work using Calibre on my office desktop, files imported and synced through Dropbox will show up exactly the same on my laptop at home provided I have the Calibre settings the same.

The same thing works for the newest version of Zotero (4.0), released last month. Zotero is a relatively simple and easy to use bibliographic citation manager that imports citations from library catalogs and databases. The citations can then be organized by folder or tagged and searched. It’s very easy to generate bibliographies in multiple formats and to add citations to things you’re writing with the MS Word plugin. It started as a Firefox add-on, but these days I use Zotero Standalone, which has connectors for Chrome, Safari, and Firefox.

It also allows you to attach a link to a file, so that if you have a citation to an article and the article stored on your computer, you can right-click the citation, choose Add Attachment, then Attach Link to File, and the linked article will appear with the citation. Then you can just click within Zotero to open the document. With version 4.0, Zotero has made a big improvement. You can now choose the “base directory” where Zotero links to the attached files. Before, you had to do it in the default directory, or attach the file itself and pay for more storage at Zotero. Not anymore. Since you can choose anywhere as the base directory, I chose my Calibre Library on Dropbox. The preferences look like this:

Once Zotero is set up like this on computers you use, the attached links to files sync when Zotero syncs, because the underlying Dropbox folder structure synchronizes across devices as well. Obviously, this could be done without using Calibre. Everything could be managed through Zotero alone, and some other Dropbox folder synced instead. But Zotero is most useful for managing citations, whereas I have lots of edocuments that I want to read and manage, but would never want to cite. By separating out the functions and using separate programs, I can get precisely what I need at any given time. Besides, files can be imported to Calibre and edited in bulk, while attaching links to files in Zotero is a slower process.

So that’s what I’m recommending as a great way to keep scholarly citations and documents stored, organized, and accessible for research.

Addendum on Evernote and Evernote Clearly

I’ve also been using the note-syncing application Evernote a lot, although I haven’t come up with any uses that are especially focused on research. You could use it for notes and quotes about sources you’re reading, but that wouldn’t be my first choice. (I use MS Word for that, and put every quote and note I have about a given source organized by title. Then I turn the title into a Heading and use the Document Map feature to easily navigate between sources.) I’ve been experimenting using it in student research consultations, where I will put the source we searched, a suggested search strategy, and maybe a citation or two, and then use the sharing feature to email the note to the student. While not scholarly, the feature that allows you to add check boxes to lists sure improved by grocery shopping. Mostly I use it to clip articles from the Internet that I want to save to read later.

Once I go read the article, I use another Evernote application called Evernote Clearly which really has to be seen to be believed. If you do a lot of online reading as I do, you should give this application a try. It’s a browser extension that reformats an online article into a pleasant, clutter-free reading experience. Plus, for a lot of articles that span multiple pages, it will reformat them all into the same page. Really, try it. Install the browser button, then navigate to this article on being an Evernote power user. Click the Clearly button and watch all the annoying clutter disappear. Your online reading experience will never be the same again.

I used Evernote for a bit but (believe it or not) found it offering too many options and I got tired of bouncing from a bunch of different software to find something. I started using Google Keep and that is simple and to the point. Three things I wish Keep had are organizing the cards order, card links, and to have the cards integrated into my Google Drive search.

I use the Drive 100gb plan and store everything in it so I can have it where ever I am. I do make sure however that I sync it to my desktop so I keep a safe copy at home. I use Google Docs to do notes for longer options such as taking notes for books or articles. Google Drive also has pdf full text searching which is handy – wish they had it for epubs too, but oh well.

I loved Clearly and that is what probably kept me on Evernote as long as I was. Now I have found Clean Print Chrome Extension. I can click that and it turns the site I am looking into a clean page optimized for printing. If I don’t like something that it kept, it gives you the option to click on it and remove it. You can also add sections back that it removed in the initial processing. The big feature I love is that it then allows you to save it right to your Google Drive account as a PDF so everything I read can be clipped right into Drive.

Right now I am not using a citation manager but have used Zotero in the past. I liked it and when I need one again I will probably go back to it.

I love Calibre and have been using that ever since I read (what I think was yours) a little over a year ago. I wish that it did a better of job of turning epubs into pdfs though because then all my documents would be full text searchable in Drive.

Thanks for the great article! You got me started thinking about a lot of these things.

It sounds like a nice setup, Adam. At the moment I’m trying hard to distribute my productivity tools among as many companies as possible, though, just so I don’t rely on Google for everything. Google’s let me down before, and I’d like to avoid Google developing products that copy others, driving out competition through cheaper prices, and then killing the products. So for now I’m using Google for products they clearly do better than everyone else (e.g., gmail) or for which there is no adequate substitute (e.g., bookmarks) or which I know they’re making money on (e.g., Android), preferably all three.

I love Evernote Clearly, but now I’m definitely going to have to try out the Clean Print extension. Sounds like it might be even better!

Thank you very match for your tips. I’m synchronizing calibre in the dropbox folder, as you suggested. I have not quite figured out how to implement also zotero: you can directly read the calibre’s metadata in zotero (and vice versa?). It would be useful to obtain metadata (perhaps modifying them) and then mention them directly in the text.
I’m sorry for my bad English (I’m Italian).

The benefit of Zotero is that it makes it easy to organize citations and create bibliographies. It could also be used like Calibre if you created a link from a Zotero citation to an edocument in Dropbox.

I use them for different purposes, though. I think Calibre is a much easier way to collect and organize PDFs and ebooks, most of which I’m not going to be using in a research project. When it comes time to gather things for an article or something, I use Zotero and link to documents.

I’ve read through your blog and I see value in the toolsets you’re recommending, but am having trouble understanding how to integrate Calibre and Zotero. Any more recent thoughts on the integration of these tools – or newer tools?

I no longer use Calibre for this purpose. Now it’s more of an ebook storage system rather than a document organizer. The newest tool I’ve been using is Scrivener, which I’m using to gather and arrange notes and quotes for a book I’m working on, along with Zotero for the citations.